I exported taxonomy information at the Class level using MEGAN, and there were 1306 contigs assigned to Mammalia. I used those 1306 sequences to re-run above scripts and only 97.6% of the 1306 sequences were assigned to Mammalia. This is not expected as I expected 100% of the 1306 sequences were assigned to Mammalia.
Then, I set --masking 0 and run the analyses again.
I used Diamond and MEGAN to assign taxonomy for my contigs.
I exported taxonomy information at the Class level using MEGAN, and there were 1306 contigs assigned to Mammalia. I used those 1306 sequences to re-run above scripts and only 97.6% of the 1306 sequences were assigned to Mammalia. This is not expected as I expected 100% of the 1306 sequences were assigned to Mammalia.
Then, I set --masking 0 and run the analyses again.
I used the contigs assigned to Mammalia to re-run the above scripts, only 82.2% sequences were assigned to Mammalia.
I am wondering what caused the inconsistency and what parameters can be used to increase the consistency for the results from different runs.